Ok, after several hours of decompiling and debugging I found that:
gg.minion.util.ConfigurationManager#xmlConfig lacks encoding set. Thus it writes configuration in windows-125X encoding and if system's locale is not en last-data-refresh value will not conform to UTF-8 when read back on next start. Just configure it xmlConfig.setEncoding("UTF-8"); and it's ok.
I guess this affects all languages were months names use non-ASCII characters.
Though I'd prefer to see a JAXB-based implementation.
AddOns Librarian, SlightlyImprovedExperienceBar, SousChef, wykkydsOutfitter have version set on site, but not in TOC. Minion has no idea about version so it assumes last. It would be better to indicate something like 'no info' to hint user to manually reinstall.
AddOns SousChef and GuildEventsImproved have version mismatch between site and TOC. Minion autoupdates them, but TOC isn't change and on next data refresh Minion proposes update again.